BMRB Entry 19876

Name: 3D structure of YmoB. A modulator of biofilm formation.
Published: 2015-03-30

Click here to enlarge.

PDB ID: 2mn2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19876
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

3D structure of YmoB. A modulator of biofilm formation.

Deposition date:

2014-03-26

Original release date:

2015-03-30

Authors:

Marimon, Oriol; Cordeiro, Tiago; Amata, Irene; Pons, Miquel

Citation:

Citation: Marimon, Oriol; Cordeiro, Tiago; Amata, Irene; Mayzel, Maxim; Orekhov, Vladislav; Wood, Thomas; Pons, Miquel. "TomB/YmoB proteins: structure and function in biofilm regulation." .

Assembly members:

Assembly members:
entity, polymer, 133 residues, 14191.914 Da.

Natural source:

Natural source: Common Name: enterobacteria Taxonomy ID: 630 Superkingdom: Bacteria Kingdom: not available Genus/species: Yersinia enterocolitica

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pHAT2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MSHHHHHHSMGMDEYSPKRH DVAQLKFLCESLYDEGIATL GDSHHGWVNDPTSAVNLQLN DLIEHIASFVMSFKIKYPDD GDLSELVEEYLDDTYTLFSS YGINDPELQRWQKTKERLFR LFSGEYISTLMKT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	505
15N chemical shifts	123
1H chemical shifts	866

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YmoB-C117S	1

Entities:

Entity 1, YmoB-C117S 133 residues - 14191.914 Da.

1

MET

SER

HIS

SER

MET

2

GLY

MET

ASP

GLU

TYR

SER

PRO

LYS

ARG

HIS

3

ASP

VAL

ALA

GLN

LEU

LYS

PHE

LEU

CYS

GLU

4

SER

LEU

TYR

ASP

GLU

GLY

ILE

ALA

THR

LEU

5

GLY

ASP

SER

HIS

GLY

TRP

VAL

ASN

ASP

6

PRO

THR

SER

ALA

VAL

ASN

LEU

GLN

LEU

ASN

7

ASP

LEU

ILE

GLU

HIS

ILE

ALA

SER

PHE

VAL

8

MET

SER

PHE

LYS

ILE

LYS

TYR

PRO

ASP

9

GLY

ASP

LEU

SER

GLU

LEU

VAL

GLU

TYR

10

LEU

ASP

THR

TYR

THR

LEU

PHE

SER

11

TYR

GLY

ILE

ASN

ASP

PRO

GLU

LEU

GLN

ARG

12

TRP

GLN

LYS

THR

LYS

GLU

ARG

LEU

PHE

ARG

13

LEU

PHE

SER

GLY

GLU

TYR

ILE

SER

THR

LEU

14

MET

LYS

THR

Samples:

sample_1: YmoB-C117S 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_2: YmoB-C117S, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_3: YmoB-C117S, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_4: YmoB-C117S, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_5: YmoB-C117S, [U-10% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.00; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_3	isotropic	sample_conditions_1
3D HN(CO)CA	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic Constant Time	sample_5	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D HccH-TOCSY	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_4	isotropic	sample_conditions_1

Software:

TOPSPIN v2.0 and 3.0, Bruker Biospin - collection

VNMRJ v3.2, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MddNMR, V. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburg - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRView, Johnson, One Moon Scientific - data analysis

Unio'10 vVersion 2.0.2, 2002-2011 Torsten Herrmann - chemical shift assignment

TALOS v+, Cornilescu, Delaglio and Bax - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.2.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

ProcheckNMR, Laskowski and MacArthur - data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

PyMol, Schr dinger, LLC. - data analysis

NMR spectrometers:

Bruker DRX 800 MHz
Varian INOVA 900 MHz
Varian INOVA 800 MHz

PDB	2MN2
EMBL	CAL13149 CBX70720 CBY26149 CCO69635 CCQ41626
GB	AAQ90016 ADZ41643 AHM72673 AJI85062 AJJ21754
REF	WP_005163463 WP_005167670 WP_050077354 YP_001007296